Abstract

Background

Escherichia coli exists in commensal and pathogenic forms. By measuring the variation of individual
genes across more than a hundred sequenced genomes, gene variation can be studied
in detail, including the number of mutations found for any given gene. This knowledge
will be useful for creating better phylogenies, for determination of molecular clocks
and for improved typing techniques.

Results

We find 3,051 gene clusters/families present in at least 95% of the genomes and 1,702
gene clusters present in 100% of the genomes. The former 'soft core' of about 3,000
gene families is perhaps more biologically relevant, especially considering that many
of these genome sequences are draft quality. The E. coli pan-genome for this set of isolates contains 16,373 gene clusters.

A core-gene tree, based on alignment and a pan-genome tree based on gene presence/absence,
maps the relatedness of the 186 sequenced E. coli genomes. The core-gene tree displays high confidence and divides the E. coli strains into the observed MLST type clades and also separates defined phylotypes.

Conclusion

The results of comparing a large and diverse E. coli dataset support the theory that reliable and good resolution phylogenies can be inferred
from the core-genome. The results further suggest that the resolution at the isolate
level may, subsequently be improved by targeting more variable genes. The use of whole
genome sequencing will make it possible to eliminate, or at least reduce, the need
for several typing steps used in traditional epidemiology.